Academic lineage
- Bernhard Ø Palsson - Ph.D. student
Whole-cell modeling of E. coli colonies enables quantification of single-cell heterogeneity in antibiotic responses
- Christopher J Skalnik, Sean Y Cheah, Mica Y Yang, …, Shayn M Peirce, Eran Agmon, Markus W Covert
- PLoS Comput Biol, 10.1371/journal.pcbi.1011232
An expanded whole-cell model of E. coli links cellular physiology with mechanisms of growth rate control
- Travis A Ahn-Horst, Luis Santiago Mille, Gwanggyu Sun, …, Gwanggyu Sun, Jerry H Morrison, Markus W Covert
- NPJ Syst Biol Appl, 10.1038/s41540-022-00242-9
Microbial metabolites in the marine carbon cycle
- Mary Ann Moran, Elizabeth B Kujawinski, William F Schroer, …, Ashley Shade, Matthew B Sullivan, Assaf Vardi
- Nat Microbiol, 10.1038/s41564-022-01090-3
A multiplexed epitope barcoding strategy that enables dynamic cellular phenotypic screens
- Takamasa Kudo, Keara Lane, Markus W Covert
- Cell Syst, 10.1016/j.cels.2022.02.006
Vivarium: an interface and engine for integrative multiscale modeling in computational biology
- Eran Agmon, Ryan K Spangler, Christopher J Skalnik, …, Shayn M Peirce, Jerry H Morrison, Markus W Covert
- Bioinformatics, 10.1093/bioinformatics/btac049
Building Structural Models of a Whole Mycoplasma Cell
- Martina Maritan, Ludovic Autin, Jonathan Karr, …, Markus W Covert, Arthur J Olson, David S Goodsell
- J Mol Biol, 10.1016/j.jmb.2021.167351
A forecast for large-scale, predictive biology: Lessons from meteorology
- Markus W Covert, Taryn E Gillies, Takamasa Kudo, Eran Agmon
- Cell Syst, 10.1016/j.cels.2021.05.014
A Protocol to Engineer Bacteriophages for Live-Cell Imaging of Bacterial Prophage Induction Inside Mammalian Cells
- Katie Bodner, Arin L Melkonian, Markus W Covert
- STAR Protoc, 10.1016/j.xpro.2020.100084
Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation
- Derek N Macklin, Travis A Ahn-Horst, Heejo Choi, …, Peter D Karp, Jerry H Morrison, Markus W Covert
- Science, 10.1126/science.aav3751
Stress-mediated exit to quiescence restricted by increasing persistence in CDK4/6 activation
- Hee Won Yang, Steven D Cappell, Ariel Jaimovich, …, Sergi Regot, Markus Covert, Tobias Meyer
- Elife, 10.7554/elife.44571
Engineered Fluorescent E. coli Lysogens Allow Live-Cell Imaging of Functional Prophage Induction Triggered inside Macrophages
- Katie Bodner, Arin L Melkonian, Angela I M Barth, Takamasa Kudo, Yu Tanouchi, Markus W Covert
- Cell Syst, 10.1016/j.cels.2020.02.006
Deep learning for cellular image analysis
- Erick Moen, Dylan Bannon, Takamasa Kudo, William Graf, Markus Covert, David Van Valen
- Nat Methods, 10.1038/s41592-019-0403-1